Contacts of the helix formed by residues 466 - 474 (chain I) in PDB entry 6KC4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 466 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464I ALA 3.3 0.8 - - - +
465I ILE* 1.3 88.8 - - - +
467I ARG* 1.3 67.5 + - - +
468I ILE* 4.0 11.7 - - + +
469I GLU* 2.9 45.8 + - + +
470I ALA* 3.0 11.3 + - - +
483I ARG* 4.3 1.3 - - - -
486I HIS* 3.9 13.9 - - + +
455K LEU* 4.4 10.3 - - + -
492K TYR* 3.6 24.7 - - + +
514K TYR* 4.0 18.8 - - - +
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Residues in contact with ARG 467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466I PRO* 1.3 72.3 - - - +
468I ILE* 1.3 65.1 + - - +
470I ALA* 3.0 4.0 + - - +
471I GLN* 3.0 23.8 + - + +
483I ARG* 3.7 23.8 - - - +
486I HIS* 5.1 0.6 + - - -
504I HIS* 3.5 36.6 - - + +
1J ASP* 3.4 41.0 + - - +
2J GLU* 2.8 34.6 + - - +
3J PTR 2.8 48.7 + - - +
509K TYR* 4.8 4.5 - - + +
512K ASN* 5.8 0.9 - - - +
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Residues in contact with ILE 468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466I PRO* 4.0 18.6 - - + +
467I ARG* 1.3 79.9 - - - +
469I GLU* 1.3 67.2 + - + +
471I GLN* 3.5 42.1 - - - +
472I GLU* 3.8 13.1 + - + +
509K TYR* 6.1 2.0 - - + +
512K ASN 6.1 0.4 - - - +
514K TYR* 4.3 14.3 + - + +
522K SER* 3.5 34.5 - - - +
523K ASN* 4.3 17.7 - - + +
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Residues in contact with GLU 469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465I ILE* 3.6 28.2 - - + +
466I PRO* 2.9 27.9 + - + +
468I ILE* 1.3 80.2 - - + +
470I ALA* 1.3 67.5 + - - +
471I GLN 3.2 0.2 - - - -
472I GLU* 3.2 17.4 + - - +
473I LEU* 3.6 16.2 + - + +
454K PRO* 3.6 23.2 - - + +
455K LEU* 2.8 43.8 + - - +
456K ALA* 5.1 1.6 + - - +
523K ASN* 6.2 1.8 - - + -
525K PRO* 5.6 1.6 - - - +
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Residues in contact with ALA 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465I ILE* 4.0 13.8 - - + +
466I PRO 3.0 6.0 + - - +
467I ARG* 3.0 8.9 + - - +
469I GLU* 1.3 77.1 - - - +
471I GLN* 1.3 63.0 + - - +
473I LEU* 3.1 12.1 + - - +
474I LEU* 3.3 20.8 + - + +
481I LEU* 4.2 13.2 - - + -
483I ARG* 3.8 32.8 - - - +
495I SER* 4.4 8.3 - - - +
504I HIS* 4.7 3.1 - - + -
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Residues in contact with GLN 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467I ARG* 3.0 13.7 + - + +
468I ILE* 3.5 32.2 - - - +
469I GLU 3.2 0.4 - - - -
470I ALA* 1.3 77.1 - - - +
472I GLU* 1.3 82.0 + - - +
473I LEU 3.3 0.2 + - - -
474I LEU 3.2 8.0 - - - +
502I ARG* 3.2 57.4 + - + +
504I HIS* 5.4 2.8 - - - +
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Residues in contact with GLU 472 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468I ILE* 3.8 15.5 - - + +
469I GLU* 3.2 9.9 + - - +
471I GLN* 1.3 101.5 + - - +
473I LEU* 1.3 61.5 - - + +
474I LEU 3.6 0.3 + - - -
475I LYS* 3.3 28.4 + - - +
502I ARG* 5.3 2.1 + - - +
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Residues in contact with LEU 473 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462I HIS* 3.6 31.6 - - + +
465I ILE* 3.8 20.9 - - + -
469I GLU* 3.7 11.4 - - + +
470I ALA 3.1 7.7 + - - +
472I GLU* 1.3 81.5 - - + +
474I LEU* 1.3 58.2 + - - +
475I LYS* 3.9 16.3 + - - +
479I ASP* 4.4 0.2 - - - +
481I LEU* 4.0 11.0 - - + -
550I ILE* 3.7 34.0 - - + +
551I PRO 5.6 1.3 - - - +
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Residues in contact with LEU 474 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470I ALA* 3.3 20.5 + - + +
471I GLN 3.2 0.5 + - - +
472I GLU 3.4 0.2 - - - -
473I LEU* 1.3 76.8 - - - +
475I LYS* 1.3 60.1 + - - +
479I ASP* 3.7 33.9 - - + +
480I PHE* 3.7 15.3 - - - +
481I LEU* 4.0 13.5 - - + -
495I SER* 3.7 36.6 - - - +
496I VAL 3.8 8.1 - - - +
497I TYR* 3.4 15.2 - - + -
502I ARG* 3.0 43.6 + - + -
504I HIS* 5.1 0.9 - - + -
550I ILE* 4.0 4.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il